rs716455

Variant names:

• chr16-61517813-C-G
• rs716455

Your query was ambiguous. Multiple possible variants found:

• chr16-61517813-C-G
• chr16-61517813-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.571 in 151,722 control chromosomes in the GnomAD database, including 24,854 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (24854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86546 AN: 151604 Hom.: 24833 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.600

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.571 AC: 86608 AN: 151722 Hom.: 24854 Cov.: 32 AF XY: 0.563 AC XY: 41687 AN XY: 74102

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.594

Alfa AF: 0.561 Hom.: 2857

Bravo AF: 0.579

Asia WGS AF: 0.462 AC: 1606 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs716455; hg19: chr16-61551717;